Starting phenix.real_space_refine
on Fri Jul  3 01:07:53 2026 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8p0g_17333/07_2026/8p0g_17333.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8p0g_17333/07_2026/8p0g_17333.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.17
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8p0g_17333/07_2026/8p0g_17333.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8p0g_17333/07_2026/8p0g_17333.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8p0g_17333/07_2026/8p0g_17333.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8p0g_17333/07_2026/8p0g_17333.map"
  }
  resolution = 3.17
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.018
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      19      5.49       5
     Mg      1      5.21       5
     S      68      5.16       5
     C    7119      2.51       5
     N    1979      2.21       5
     O    2145      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 11331
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3644
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 453, 3644
          Classifications: {'peptide': 453}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 26, 'TRANS': 426}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 5307
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 662, 5307
          Classifications: {'peptide': 662}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 628}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "C"
      Number of atoms: 1966
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 241, 1954
          Classifications: {'peptide': 241}
          Link IDs: {'PTRANS': 16, 'TRANS': 224}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 241, 1954
          Classifications: {'peptide': 241}
          Link IDs: {'PTRANS': 16, 'TRANS': 224}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 1989
    Chain: "V"
      Number of atoms: 307
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 307
          Classifications: {'RNA': 14}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 8, 'rna3p_pyr': 3}
          Link IDs: {'rna2p': 3, 'rna3p': 10}
    Chain: "R"
      Number of atoms: 106
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 106
          Classifications: {'RNA': 5}
          Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 3}
          Link IDs: {'rna3p': 4}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ATYR C  59 " occ=0.50
      ... (22 atoms not shown)
      pdb=" OH BTYR C  59 " occ=0.50
  Time building chain proxies: 2.23, per 1000 atoms: 0.20
  Number of scatterers: 11331
  At special positions: 0
  Unit cell: (102.548, 110.818, 95.932, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      68     16.00
     P      19     15.00
     Mg      1     11.99
     O    2145      8.00
     N    1979      7.00
     C    7119      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.81
  Conformation dependent library (CDL) restraints added in 490.1 milliseconds
  

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2588

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 16 sheets defined
      50.9% alpha, 10.2% beta
      5 base pairs and 12 stacking pairs defined.
    Time for finding SS restraints: 1.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 176 through 184
    Processing helix  chain 'A' and resid 246 through 257
    Processing helix  chain 'A' and resid 270 through 272
      No H-bonds generated for 'chain 'A' and resid 270 through 272'
    Processing helix  chain 'A' and resid 273 through 286
      removed outlier: 3.706A  pdb=" N   LEU A 277 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 301
    Processing helix  chain 'A' and resid 304 through 316
      removed outlier: 3.715A  pdb=" N   GLU A 308 " --> pdb=" O   ASN A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 345
      removed outlier: 4.215A  pdb=" N   GLU A 339 " --> pdb=" O   PRO A 335 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   ARG A 345 " --> pdb=" O   MET A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 381
      removed outlier: 4.555A  pdb=" N   ARG A 381 " --> pdb=" O   GLU A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 401
    Processing helix  chain 'A' and resid 485 through 493
    Processing helix  chain 'A' and resid 494 through 497
    Processing helix  chain 'A' and resid 498 through 515
      removed outlier: 3.615A  pdb=" N   ILE A 504 " --> pdb=" O   GLN A 500 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   GLU A 515 " --> pdb=" O   SER A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 540 through 557
    Processing helix  chain 'A' and resid 559 through 581
      removed outlier: 4.356A  pdb=" N   ARG A 571 " --> pdb=" O   ALA A 567 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   LEU A 572 " --> pdb=" O   ASN A 568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 592 through 599
      removed outlier: 3.532A  pdb=" N   GLU A 599 " --> pdb=" O   ASP A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 617
    Processing helix  chain 'B' and resid 13 through 20
      removed outlier: 4.024A  pdb=" N   GLU B  17 " --> pdb=" O   THR B  14 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 33 through 49
      Proline residue:  B  44  - end of helix
      removed outlier: 4.453A  pdb=" N   TYR B  49 " --> pdb=" O   TYR B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 58
      removed outlier: 3.609A  pdb=" N   ALA B  57 " --> pdb=" O   ASN B  53 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 70
    Processing helix  chain 'B' and resid 80 through 95
    Processing helix  chain 'B' and resid 95 through 108
    Processing helix  chain 'B' and resid 109 through 113
    Processing helix  chain 'B' and resid 114 through 121
    Processing helix  chain 'B' and resid 134 through 151
    Processing helix  chain 'B' and resid 157 through 171
      removed outlier: 3.843A  pdb=" N   GLU B 170 " --> pdb=" O   ALA B 166 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   LEU B 171 " --> pdb=" O   ASP B 167 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 225
    Processing helix  chain 'B' and resid 247 through 249
      No H-bonds generated for 'chain 'B' and resid 247 through 249'
    Processing helix  chain 'B' and resid 250 through 266
    Processing helix  chain 'B' and resid 277 through 287
    Processing helix  chain 'B' and resid 310 through 326
      removed outlier: 3.655A  pdb=" N   MET B 314 " --> pdb=" O   ASP B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 328 through 344
      Proline residue:  B 338  - end of helix
    Processing helix  chain 'B' and resid 373 through 380
      removed outlier: 4.454A  pdb=" N   ARG B 378 " --> pdb=" O   ASP B 375 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   VAL B 380 " --> pdb=" O   VAL B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 397 through 409
      removed outlier: 3.710A  pdb=" N   SER B 407 " --> pdb=" O   LEU B 403 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   ILE B 408 " --> pdb=" O   ALA B 404 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   GLU B 409 " --> pdb=" O   LEU B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 451
    Processing helix  chain 'B' and resid 496 through 514
    Processing helix  chain 'B' and resid 518 through 537
    Processing helix  chain 'B' and resid 543 through 552
    Processing helix  chain 'B' and resid 558 through 562
    Processing helix  chain 'B' and resid 575 through 583
    Processing helix  chain 'B' and resid 587 through 596
    Processing helix  chain 'B' and resid 646 through 666
      removed outlier: 4.143A  pdb=" N   ASN B 650 " --> pdb=" O   LYS B 646 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   LYS B 651 " --> pdb=" O   ALA B 647 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 679 through 694
    Processing helix  chain 'B' and resid 698 through 708
      removed outlier: 3.510A  pdb=" N   ARG B 708 " --> pdb=" O   ARG B 704 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 8 through 27
    Processing helix  chain 'C' and resid 27 through 32
      removed outlier: 3.667A  pdb=" N   SER C  32 " --> pdb=" O   PRO C  28 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 33 through 35
      No H-bonds generated for 'chain 'C' and resid 33 through 35'
    Processing helix  chain 'C' and resid 36 through 42
      removed outlier: 4.136A  pdb=" N   THR C  40 " --> pdb=" O   THR C  36 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 52 through 62
      removed outlier: 3.706A  pdb=" N   ARG C  56 " --> pdb=" O   ALA C  52 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   VAL C  58 " --> pdb=" O   GLN C  54 " (cutoff:3.500A)
      removed outlier: 4.981A  pdb=" N  ATYR C  59 " --> pdb=" O   MET C  55 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 101 through 108
      removed outlier: 4.303A  pdb=" N   ASP C 105 " --> pdb=" O   ILE C 101 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 115 through 123
    Processing helix  chain 'C' and resid 123 through 135
    Processing helix  chain 'C' and resid 163 through 165
      No H-bonds generated for 'chain 'C' and resid 163 through 165'
    Processing helix  chain 'C' and resid 166 through 176
    Processing helix  chain 'C' and resid 177 through 180
      removed outlier: 3.834A  pdb=" N   THR C 180 " --> pdb=" O   PRO C 177 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 177 through 180'
    Processing helix  chain 'C' and resid 181 through 186
    Processing helix  chain 'C' and resid 189 through 200
    Processing helix  chain 'C' and resid 208 through 221
      removed outlier: 3.816A  pdb=" N   HIS C 214 " --> pdb=" O   GLU C 210 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 234 through 245
      removed outlier: 4.077A  pdb=" N   MET C 240 " --> pdb=" O   ARG C 236 " (cutoff:3.500A)
      removed outlier: 5.384A  pdb=" N   HIS C 242 " --> pdb=" O   ALA C 238 " (cutoff:3.500A)
      removed outlier: 7.152A  pdb=" N   PHE C 243 " --> pdb=" O   GLU C 239 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   LEU C 244 " --> pdb=" O   MET C 240 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   CYS C 245 " --> pdb=" O   ALA C 241 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 240 through 242
      removed outlier: 7.585A  pdb=" N   TRP A 426 " --> pdb=" O   ILE A 450 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   LEU A 475 " --> pdb=" O   MET A 451 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   VAL A 464 " --> pdb=" O   ILE A 263 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 240 through 242
      removed outlier: 6.840A  pdb=" N   ILE A 414 " --> pdb=" O   TRP A 426 " (cutoff:3.500A)
      removed outlier: 5.364A  pdb=" N   MET A 428 " --> pdb=" O   CYS A 412 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   CYS A 412 " --> pdb=" O   MET A 428 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   LEU A 430 " --> pdb=" O   THR A 410 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   THR A 410 " --> pdb=" O   LEU A 430 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 322 through 323
      removed outlier: 3.531A  pdb=" N   LYS A 322 " --> pdb=" O   THR B 356 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 442 through 445
    Processing sheet with id=AA5, first strand: chain 'A' and resid 526 through 528
    Processing sheet with id=AA6, first strand: chain 'A' and resid 584 through 586
    Processing sheet with id=AA7, first strand: chain 'B' and resid 124 through 126
      removed outlier: 3.648A  pdb=" N   ARG B 131 " --> pdb=" O   SER B 126 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 173 through 178
    Processing sheet with id=AA9, first strand: chain 'B' and resid 227 through 230
    Processing sheet with id=AB1, first strand: chain 'B' and resid 302 through 303
      removed outlier: 4.712A  pdb=" N   ASN B 453 " --> pdb=" O   GLU B 303 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 345 through 348
      removed outlier: 3.619A  pdb=" N   LYS B 345 " --> pdb=" O   CYS B 387 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 467 through 470
    Processing sheet with id=AB4, first strand: chain 'C' and resid 67 through 69
    Processing sheet with id=AB5, first strand: chain 'C' and resid 78 through 79
    Processing sheet with id=AB6, first strand: chain 'C' and resid 142 through 143
    Processing sheet with id=AB7, first strand: chain 'C' and resid 150 through 154

    523 hydrogen bonds defined for protein.
    1441 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      14 hydrogen bonds
      28 hydrogen bond angles
      0 basepair planarities
      5 basepair parallelities
      12 stacking parallelities
  Total time for adding SS restraints: 1.61

  Time building geometry restraints manager: 1.13 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.34: 3620
        1.34 -     1.46: 1723
        1.46 -     1.57: 6124
        1.57 -     1.69: 36
        1.69 -     1.81: 114
  Bond restraints: 11617
  Sorted by residual:
  bond pdb=" N   MET B   1 "
       pdb=" CA  MET B   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.91e+00
  bond pdb=" CB  PRO B 464 "
       pdb=" CG  PRO B 464 "
    ideal  model  delta    sigma   weight residual
    1.506  1.477  0.029 3.90e-02 6.57e+02 5.35e-01
  bond pdb=" C   LEU A 171 "
       pdb=" N   GLN A 172 "
    ideal  model  delta    sigma   weight residual
    1.332  1.322  0.010 1.40e-02 5.10e+03 5.21e-01
  bond pdb=" C   GLU C 201 "
       pdb=" N   PRO C 202 "
    ideal  model  delta    sigma   weight residual
    1.334  1.350 -0.016 2.34e-02 1.83e+03 4.85e-01
  bond pdb=" CB  PRO B 274 "
       pdb=" CG  PRO B 274 "
    ideal  model  delta    sigma   weight residual
    1.492  1.526 -0.034 5.00e-02 4.00e+02 4.59e-01
  ... (remaining 11612 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.98: 15402
        0.98 -     1.96: 298
        1.96 -     2.94: 51
        2.94 -     3.92: 51
        3.92 -     4.89: 8
  Bond angle restraints: 15810
  Sorted by residual:
  angle pdb=" C1'   C R  21 "
        pdb=" N1    C R  21 "
        pdb=" C2    C R  21 "
      ideal   model   delta    sigma   weight residual
     118.80  121.58   -2.78 1.10e+00 8.26e-01 6.40e+00
  angle pdb=" N   GLU C 201 "
        pdb=" CA  GLU C 201 "
        pdb=" C   GLU C 201 "
      ideal   model   delta    sigma   weight residual
     109.81  114.70   -4.89 2.21e+00 2.05e-01 4.89e+00
  angle pdb=" C   ASP A 405 "
        pdb=" N   ARG A 406 "
        pdb=" CA  ARG A 406 "
      ideal   model   delta    sigma   weight residual
     121.54  125.43   -3.89 1.91e+00 2.74e-01 4.15e+00
  angle pdb=" C1'   C R  21 "
        pdb=" N1    C R  21 "
        pdb=" C6    C R  21 "
      ideal   model   delta    sigma   weight residual
     120.80  118.54    2.26 1.20e+00 6.94e-01 3.54e+00
  angle pdb=" N1    C R  21 "
        pdb=" C2    C R  21 "
        pdb=" O2    C R  21 "
      ideal   model   delta    sigma   weight residual
     118.90  119.98   -1.08 6.00e-01 2.78e+00 3.23e+00
  ... (remaining 15805 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.71: 6162
       16.71 -    33.42: 698
       33.42 -    50.13: 177
       50.13 -    66.84: 68
       66.84 -    83.55: 18
  Dihedral angle restraints: 7123
    sinusoidal: 3138
      harmonic: 3985
  Sorted by residual:
  dihedral pdb=" CA  GLU C 201 "
           pdb=" C   GLU C 201 "
           pdb=" N   PRO C 202 "
           pdb=" CA  PRO C 202 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.62  -22.38     0      5.00e+00 4.00e-02 2.00e+01
  dihedral pdb=" CG  ARG B 581 "
           pdb=" CD  ARG B 581 "
           pdb=" NE  ARG B 581 "
           pdb=" CZ  ARG B 581 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  135.06   44.94     2      1.50e+01 4.44e-03 1.06e+01
  dihedral pdb=" CG  ARG A 323 "
           pdb=" CD  ARG A 323 "
           pdb=" NE  ARG A 323 "
           pdb=" CZ  ARG A 323 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  135.58   44.42     2      1.50e+01 4.44e-03 1.04e+01
  ... (remaining 7120 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1165
       0.028 -    0.055: 423
       0.055 -    0.083: 90
       0.083 -    0.110: 73
       0.110 -    0.138: 23
  Chirality restraints: 1774
  Sorted by residual:
  chirality pdb=" CA  VAL B 491 "
            pdb=" N   VAL B 491 "
            pdb=" C   VAL B 491 "
            pdb=" CB  VAL B 491 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.74e-01
  chirality pdb=" CA  ILE A 192 "
            pdb=" N   ILE A 192 "
            pdb=" C   ILE A 192 "
            pdb=" CB  ILE A 192 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.66e-01
  chirality pdb=" CA  ILE A 527 "
            pdb=" N   ILE A 527 "
            pdb=" C   ILE A 527 "
            pdb=" CB  ILE A 527 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.02e-01
  ... (remaining 1771 not shown)

  Planarity restraints: 1953
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A V   7 "    0.017 2.00e-02 2.50e+03   7.91e-03 1.72e+00
        pdb=" N9    A V   7 "   -0.019 2.00e-02 2.50e+03
        pdb=" C8    A V   7 "   -0.001 2.00e-02 2.50e+03
        pdb=" N7    A V   7 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    A V   7 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    A V   7 "    0.002 2.00e-02 2.50e+03
        pdb=" N6    A V   7 "    0.004 2.00e-02 2.50e+03
        pdb=" N1    A V   7 "    0.001 2.00e-02 2.50e+03
        pdb=" C2    A V   7 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    A V   7 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    A V   7 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU C 201 "   -0.021 5.00e-02 4.00e+02   3.14e-02 1.58e+00
        pdb=" N   PRO C 202 "    0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO C 202 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C 202 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B  96 "    0.020 5.00e-02 4.00e+02   2.98e-02 1.42e+00
        pdb=" N   PRO B  97 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO B  97 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B  97 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1950 not shown)

  Histogram of nonbonded interaction distances:
        1.96 -     2.55: 100
        2.55 -     3.14: 8783
        3.14 -     3.73: 17692
        3.73 -     4.31: 24963
        4.31 -     4.90: 42634
  Nonbonded interactions: 94172
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 423 "
            pdb="MG    MG B 801 "
     model   vdw
     1.965 2.170
  nonbonded pdb=" OD1 ASN A 516 "
            pdb=" OG  SER A 518 "
     model   vdw
     2.070 3.040
  nonbonded pdb=" OE1 GLU C  74 "
            pdb=" OG  SER C 112 "
     model   vdw
     2.144 3.040
  nonbonded pdb=" OE1 GLU A 369 "
            pdb=" NH2 ARG B 527 "
     model   vdw
     2.168 3.120
  nonbonded pdb=" OG1 THR B  62 "
            pdb=" OD2 ASP B 312 "
     model   vdw
     2.220 3.040
  ... (remaining 94167 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     10.250
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  11617  Z= 0.091
  Angle     :  0.417   4.895  15810  Z= 0.222
  Chirality :  0.036   0.138   1774
  Planarity :  0.003   0.031   1953
  Dihedral  : 16.061  83.552   4535
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  3.65 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  : 12.29 %
    Favored  : 87.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.93 (0.24), residues: 1345
  helix:  2.17 (0.22), residues: 625
  sheet: -0.44 (0.44), residues: 127
  loop : -0.87 (0.26), residues: 593

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 198 
 TYR   0.013   0.001   TYR B  22 
 PHE   0.015   0.001   PHE C  41 
 TRP   0.005   0.001   TRP A 336 
 HIS   0.002   0.000   HIS B 291 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00196 /  0.09 (11617)
  covalent geometry    : angle       0.41651 /  0.22 (15810)
  hydrogen bonds       : bond        0.14411 /  9.81 (  533)
  hydrogen bonds       : angle       5.37939 /  3.92 ( 1469)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 127
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  101 ILE cc_start: 0.8204 (pt) cc_final: 0.7930 (tt)
  outliers start: 2
  outliers final: 2
  residues processed: 129
  average time/residue: 0.1377
  time to fit residues: 23.3694
Evaluate side-chains
  72 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 70
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  483 PHE
Chi-restraints excluded: chain B residue  289 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    0.0070
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:    0.0870
   chunk 77 optimal weight:    9.9990
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    7.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    2.0182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 453 ASN
B 582 HIS
C 131 GLN
C 242 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.052581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.040136 restraints weight = 72677.629|
|-----------------------------------------------------------------------------|
r_work (start): 0.2773 rms_B_bonded: 4.08
r_work: 0.2613 rms_B_bonded: 4.60 restraints_weight: 0.5000
r_work (final): 0.2613
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2619
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2619 r_free = 0.2619    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2619 r_free = 0.2619    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2619
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8951
moved from start:          0.1416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  11617  Z= 0.193
  Angle     :  0.574   7.930  15810  Z= 0.297
  Chirality :  0.040   0.212   1774
  Planarity :  0.005   0.064   1953
  Dihedral  :  9.751  73.357   1771
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  3.58 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 14.36 %
    Favored  : 83.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.92 (0.24), residues: 1345
  helix:  2.19 (0.22), residues: 616
  sheet: -0.56 (0.44), residues: 127
  loop : -0.82 (0.25), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 701 
 TYR   0.023   0.002   TYR B 533 
 PHE   0.025   0.002   PHE C  41 
 TRP   0.012   0.001   TRP A 253 
 HIS   0.006   0.001   HIS A 434 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00447 /  0.19 (11617)
  covalent geometry    : angle       0.57385 /  0.30 (15810)
  hydrogen bonds       : bond        0.04435 /  2.97 (  533)
  hydrogen bonds       : angle       4.68340 /  3.37 ( 1469)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 76
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   11 CYS cc_start: 0.9247 (m) cc_final: 0.8997 (p)
  outliers start: 21
  outliers final: 12
  residues processed: 89
  average time/residue: 0.0874
  time to fit residues: 11.5165
Evaluate side-chains
  81 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  289 THR
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  395 MET
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain C residue   73 LYS
Chi-restraints excluded: chain C residue  181 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 135 optimal weight:   10.0000
   chunk 121 optimal weight:    4.9990
   chunk 71 optimal weight:    0.5980
   chunk 62 optimal weight:    8.9990
   chunk 0 optimal weight:    8.9990
   chunk 75 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9980
   chunk 89 optimal weight:    6.9990
   chunk 50 optimal weight:    0.9990
   chunk 97 optimal weight:    4.9990
   chunk 126 optimal weight:    0.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 214 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.052338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.040310 restraints weight = 72478.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.2780 rms_B_bonded: 4.01
r_work: 0.2622 rms_B_bonded: 4.51 restraints_weight: 0.5000
r_work (final): 0.2622
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2627
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2627 r_free = 0.2627    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2627 r_free = 0.2627    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2627
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8941
moved from start:          0.1678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11617  Z= 0.141
  Angle     :  0.519   6.415  15810  Z= 0.266
  Chirality :  0.039   0.176   1774
  Planarity :  0.004   0.040   1953
  Dihedral  :  9.648  73.310   1769
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  3.65 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 14.11 %
    Favored  : 83.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.82 (0.23), residues: 1345
  helix:  2.05 (0.21), residues: 623
  sheet: -0.63 (0.43), residues: 125
  loop : -0.82 (0.25), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  43 
 TYR   0.021   0.001   TYR B 533 
 PHE   0.026   0.001   PHE C  41 
 TRP   0.010   0.001   TRP A 253 
 HIS   0.006   0.001   HIS B 291 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.14 (11617)
  covalent geometry    : angle       0.51855 /  0.27 (15810)
  hydrogen bonds       : bond        0.03797 /  2.55 (  533)
  hydrogen bonds       : angle       4.43928 /  3.19 ( 1469)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 70
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   11 CYS cc_start: 0.9252 (m) cc_final: 0.8949 (p)
  outliers start: 29
  outliers final: 13
  residues processed: 92
  average time/residue: 0.0857
  time to fit residues: 12.1535
Evaluate side-chains
  80 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  574 MET
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  289 THR
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  407 SER
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  652 GLU
Chi-restraints excluded: chain C residue   73 LYS
Chi-restraints excluded: chain C residue  146 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 52 optimal weight:    4.9990
   chunk 21 optimal weight:    6.9990
   chunk 61 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 111 optimal weight:    0.0970
   chunk 34 optimal weight:    0.0570
   chunk 14 optimal weight:    2.9990
   chunk 119 optimal weight:    6.9990
   chunk 132 optimal weight:    3.9990
   chunk 57 optimal weight:   10.0000
   chunk 47 optimal weight:    2.9990
   overall best weight:    1.3900

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.052006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.040120 restraints weight = 66509.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.2776 rms_B_bonded: 3.83
r_work: 0.2623 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.2623
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2629
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2629 r_free = 0.2629    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2629 r_free = 0.2629    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2629
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8945
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11617  Z= 0.141
  Angle     :  0.515   6.614  15810  Z= 0.263
  Chirality :  0.039   0.175   1774
  Planarity :  0.004   0.042   1953
  Dihedral  :  9.644  73.297   1769
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  4.40 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 14.11 %
    Favored  : 83.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.85 (0.23), residues: 1345
  helix:  2.02 (0.21), residues: 625
  sheet: -0.58 (0.43), residues: 125
  loop : -0.77 (0.26), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  43 
 TYR   0.020   0.001   TYR B 533 
 PHE   0.026   0.001   PHE C  41 
 TRP   0.009   0.001   TRP A 336 
 HIS   0.006   0.001   HIS B 291 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00328 /  0.14 (11617)
  covalent geometry    : angle       0.51517 /  0.26 (15810)
  hydrogen bonds       : bond        0.03592 /  2.41 (  533)
  hydrogen bonds       : angle       4.35294 /  3.12 ( 1469)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 67
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  617 MET cc_start: 0.9313 (mtm) cc_final: 0.8983 (mtm)
REVERT: C   11 CYS cc_start: 0.9237 (m) cc_final: 0.8940 (p)
  outliers start: 29
  outliers final: 19
  residues processed: 86
  average time/residue: 0.0703
  time to fit residues: 9.5930
Evaluate side-chains
  86 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 67
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  286 GLU
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  574 MET
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   32 THR
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  395 MET
Chi-restraints excluded: chain B residue  399 THR
Chi-restraints excluded: chain B residue  407 SER
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  652 GLU
Chi-restraints excluded: chain C residue   73 LYS
Chi-restraints excluded: chain C residue  146 MET
Chi-restraints excluded: chain C residue  181 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 18 optimal weight:    4.9990
   chunk 1 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9990
   chunk 54 optimal weight:    0.6980
   chunk 115 optimal weight:    7.9990
   chunk 38 optimal weight:    5.9990
   chunk 42 optimal weight:    0.7980
   chunk 98 optimal weight:    2.9990
   chunk 3 optimal weight:    0.0970
   chunk 116 optimal weight:    4.9990
   overall best weight:    1.1182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.052143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.039873 restraints weight = 88700.804|
|-----------------------------------------------------------------------------|
r_work (start): 0.2769 rms_B_bonded: 4.43
r_work: 0.2601 rms_B_bonded: 4.88 restraints_weight: 0.5000
r_work (final): 0.2601
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2605
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2605 r_free = 0.2605    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2605 r_free = 0.2605    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2605
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8957
moved from start:          0.1973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11617  Z= 0.123
  Angle     :  0.496   7.092  15810  Z= 0.253
  Chirality :  0.038   0.154   1774
  Planarity :  0.004   0.043   1953
  Dihedral  :  9.604  73.277   1768
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  4.55 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 14.85 %
    Favored  : 82.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.94 (0.24), residues: 1345
  helix:  2.12 (0.21), residues: 620
  sheet: -0.49 (0.43), residues: 125
  loop : -0.73 (0.26), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 701 
 TYR   0.019   0.001   TYR B 533 
 PHE   0.028   0.001   PHE C  41 
 TRP   0.009   0.001   TRP A 336 
 HIS   0.006   0.001   HIS B 291 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.12 (11617)
  covalent geometry    : angle       0.49643 /  0.25 (15810)
  hydrogen bonds       : bond        0.03419 /  2.30 (  533)
  hydrogen bonds       : angle       4.30270 /  3.08 ( 1469)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 69
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   11 CYS cc_start: 0.9239 (m) cc_final: 0.8925 (p)
REVERT: C  101 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.7919 (tt)
  outliers start: 29
  outliers final: 21
  residues processed: 87
  average time/residue: 0.0818
  time to fit residues: 11.2328
Evaluate side-chains
  89 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 67
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  526 GLU
Chi-restraints excluded: chain A residue  574 MET
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   32 THR
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  395 MET
Chi-restraints excluded: chain B residue  407 SER
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  649 LEU
Chi-restraints excluded: chain B residue  652 GLU
Chi-restraints excluded: chain C residue   73 LYS
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  146 MET
Chi-restraints excluded: chain C residue  181 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 29 optimal weight:    6.9990
   chunk 115 optimal weight:    7.9990
   chunk 12 optimal weight:    5.9990
   chunk 31 optimal weight:    6.9990
   chunk 90 optimal weight:    0.9980
   chunk 17 optimal weight:    0.0000
   chunk 52 optimal weight:    3.9990
   chunk 127 optimal weight:    7.9990
   chunk 110 optimal weight:    9.9990
   chunk 48 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   overall best weight:    2.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.050480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2735 r_free = 0.2735 target = 0.038344 restraints weight = 88688.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.2719 rms_B_bonded: 4.37
r_work: 0.2550 rms_B_bonded: 4.78 restraints_weight: 0.5000
r_work (final): 0.2550
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2554
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2554 r_free = 0.2554    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2554 r_free = 0.2554    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2554
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9001
moved from start:          0.2137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  11617  Z= 0.232
  Angle     :  0.555   8.144  15810  Z= 0.282
  Chirality :  0.041   0.163   1774
  Planarity :  0.004   0.040   1953
  Dihedral  :  9.636  73.218   1768
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.99 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 15.35 %
    Favored  : 81.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.23), residues: 1345
  helix:  2.06 (0.21), residues: 618
  sheet: -0.40 (0.43), residues: 121
  loop : -0.80 (0.25), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 198 
 TYR   0.023   0.001   TYR B 533 
 PHE   0.027   0.002   PHE C  41 
 TRP   0.009   0.001   TRP B 230 
 HIS   0.006   0.001   HIS B 291 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00533 /  0.23 (11617)
  covalent geometry    : angle       0.55457 /  0.28 (15810)
  hydrogen bonds       : bond        0.03879 /  2.61 (  533)
  hydrogen bonds       : angle       4.40860 /  3.14 ( 1469)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 66
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  569 MET cc_start: 0.9356 (mmm) cc_final: 0.8860 (tpp)
REVERT: A  604 ASN cc_start: 0.9287 (OUTLIER) cc_final: 0.9012 (t0)
REVERT: A  617 MET cc_start: 0.9387 (mtm) cc_final: 0.8945 (mtm)
REVERT: C  101 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8096 (tt)
  outliers start: 33
  outliers final: 23
  residues processed: 88
  average time/residue: 0.0807
  time to fit residues: 11.4403
Evaluate side-chains
  90 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 65
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  483 PHE
Chi-restraints excluded: chain A residue  574 MET
Chi-restraints excluded: chain A residue  604 ASN
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   32 THR
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  395 MET
Chi-restraints excluded: chain B residue  399 THR
Chi-restraints excluded: chain B residue  407 SER
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  620 ILE
Chi-restraints excluded: chain B residue  649 LEU
Chi-restraints excluded: chain B residue  652 GLU
Chi-restraints excluded: chain C residue   73 LYS
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  146 MET
Chi-restraints excluded: chain C residue  181 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9990
   chunk 75 optimal weight:    0.8980
   chunk 98 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0040
   chunk 45 optimal weight:    0.9980
   chunk 0 optimal weight:    7.9990
   chunk 85 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0370
   chunk 47 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.5470

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.051857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.039780 restraints weight = 76625.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.2771 rms_B_bonded: 4.14
r_work: 0.2606 rms_B_bonded: 4.66 restraints_weight: 0.5000
r_work (final): 0.2606
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2610
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2610 r_free = 0.2610    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2610 r_free = 0.2610    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2610
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8961
moved from start:          0.2192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  11617  Z= 0.105
  Angle     :  0.506   9.150  15810  Z= 0.257
  Chirality :  0.038   0.145   1774
  Planarity :  0.004   0.044   1953
  Dihedral  :  9.629  73.176   1768
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.95 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 15.68 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.97 (0.23), residues: 1345
  helix:  2.13 (0.21), residues: 619
  sheet: -0.34 (0.43), residues: 121
  loop : -0.74 (0.25), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 701 
 TYR   0.018   0.001   TYR B 533 
 PHE   0.030   0.001   PHE C  41 
 TRP   0.010   0.001   TRP A 336 
 HIS   0.006   0.001   HIS B 291 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00236 /  0.10 (11617)
  covalent geometry    : angle       0.50595 /  0.26 (15810)
  hydrogen bonds       : bond        0.03325 /  2.23 (  533)
  hydrogen bonds       : angle       4.28254 /  3.07 ( 1469)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 69
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  617 MET cc_start: 0.9273 (mtm) cc_final: 0.8878 (mtm)
REVERT: B  652 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8510 (tt0)
REVERT: C  101 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8056 (tt)
  outliers start: 25
  outliers final: 16
  residues processed: 85
  average time/residue: 0.0712
  time to fit residues: 9.8387
Evaluate side-chains
  86 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 68
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  574 MET
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   32 THR
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  395 MET
Chi-restraints excluded: chain B residue  407 SER
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain B residue  620 ILE
Chi-restraints excluded: chain B residue  649 LEU
Chi-restraints excluded: chain B residue  652 GLU
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  146 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 88 optimal weight:    3.9990
   chunk 93 optimal weight:    0.5980
   chunk 69 optimal weight:    0.0870
   chunk 112 optimal weight:    1.9990
   chunk 129 optimal weight:    4.9990
   chunk 6 optimal weight:    8.9990
   chunk 53 optimal weight:    4.9990
   chunk 130 optimal weight:    2.9990
   chunk 121 optimal weight:    0.8980
   chunk 47 optimal weight:    0.0270
   chunk 83 optimal weight:    2.9990
   overall best weight:    0.7218

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.052065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.039329 restraints weight = 100045.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.2757 rms_B_bonded: 4.81
r_work (final): 0.2757
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2757
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2757 r_free = 0.2757    target_work(ls_wunit_k1) = 0.039         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2757 r_free = 0.2757    target_work(ls_wunit_k1) = 0.039         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2757
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8893
moved from start:          0.2252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  11617  Z= 0.105
  Angle     :  0.503  10.810  15810  Z= 0.252
  Chirality :  0.038   0.226   1774
  Planarity :  0.004   0.045   1953
  Dihedral  :  9.609  73.215   1768
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 16.09 %
    Favored  : 82.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.99 (0.23), residues: 1345
  helix:  2.16 (0.21), residues: 619
  sheet: -0.30 (0.43), residues: 121
  loop : -0.74 (0.25), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  43 
 TYR   0.017   0.001   TYR B 533 
 PHE   0.030   0.001   PHE C  41 
 TRP   0.009   0.001   TRP A 336 
 HIS   0.006   0.001   HIS B 291 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00239 /  0.11 (11617)
  covalent geometry    : angle       0.50251 /  0.25 (15810)
  hydrogen bonds       : bond        0.03228 /  2.17 (  533)
  hydrogen bonds       : angle       4.25462 /  3.04 ( 1469)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 70
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  617 MET cc_start: 0.8913 (mtm) cc_final: 0.8582 (mtm)
REVERT: B  652 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8460 (tt0)
REVERT: C  101 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7887 (tt)
  outliers start: 23
  outliers final: 18
  residues processed: 84
  average time/residue: 0.0743
  time to fit residues: 9.8512
Evaluate side-chains
  88 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 68
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  574 MET
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   32 THR
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  395 MET
Chi-restraints excluded: chain B residue  407 SER
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain B residue  620 ILE
Chi-restraints excluded: chain B residue  649 LEU
Chi-restraints excluded: chain B residue  652 GLU
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  146 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 10 optimal weight:    0.0060
   chunk 130 optimal weight:    5.9990
   chunk 135 optimal weight:   10.0000
   chunk 118 optimal weight:    6.9990
   chunk 81 optimal weight:    5.9990
   chunk 111 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 122 optimal weight:    0.9980
   chunk 128 optimal weight:   10.0000
   chunk 61 optimal weight:    1.9990
   chunk 120 optimal weight:    3.9990
   overall best weight:    2.0002

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.050878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2749 r_free = 0.2749 target = 0.038647 restraints weight = 92872.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.2733 rms_B_bonded: 4.50
r_work: 0.2563 rms_B_bonded: 4.90 restraints_weight: 0.5000
r_work (final): 0.2563
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2568
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2568 r_free = 0.2568    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2568 r_free = 0.2568    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2568
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8991
moved from start:          0.2313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  11617  Z= 0.177
  Angle     :  0.550  11.671  15810  Z= 0.274
  Chirality :  0.039   0.220   1774
  Planarity :  0.004   0.041   1953
  Dihedral  :  9.633  73.179   1768
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 15.84 %
    Favored  : 82.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.97 (0.23), residues: 1345
  helix:  2.16 (0.21), residues: 619
  sheet: -0.33 (0.43), residues: 121
  loop : -0.79 (0.25), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  43 
 TYR   0.021   0.001   TYR B 533 
 PHE   0.029   0.001   PHE C  41 
 TRP   0.010   0.001   TRP B 230 
 HIS   0.006   0.001   HIS B 291 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00411 /  0.18 (11617)
  covalent geometry    : angle       0.55022 /  0.27 (15810)
  hydrogen bonds       : bond        0.03515 /  2.36 (  533)
  hydrogen bonds       : angle       4.29270 /  3.06 ( 1469)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 68
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  569 MET cc_start: 0.9329 (mmm) cc_final: 0.8808 (tpp)
REVERT: A  604 ASN cc_start: 0.9284 (OUTLIER) cc_final: 0.9014 (t0)
REVERT: A  617 MET cc_start: 0.9304 (mtm) cc_final: 0.8899 (mtm)
REVERT: C  101 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8118 (tt)
  outliers start: 26
  outliers final: 21
  residues processed: 85
  average time/residue: 0.0687
  time to fit residues: 9.5735
Evaluate side-chains
  91 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 68
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  483 PHE
Chi-restraints excluded: chain A residue  574 MET
Chi-restraints excluded: chain A residue  604 ASN
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   32 THR
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  395 MET
Chi-restraints excluded: chain B residue  399 THR
Chi-restraints excluded: chain B residue  407 SER
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain B residue  649 LEU
Chi-restraints excluded: chain B residue  652 GLU
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  146 MET
Chi-restraints excluded: chain C residue  181 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 94 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 96 optimal weight:    0.5980
   chunk 104 optimal weight:    9.9990
   chunk 98 optimal weight:    3.9990
   chunk 114 optimal weight:    2.9990
   chunk 131 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    1.0782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  51 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.051561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2759 r_free = 0.2759 target = 0.039016 restraints weight = 93282.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.2748 rms_B_bonded: 4.62
r_work (final): 0.2748
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2748
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2748 r_free = 0.2748    target_work(ls_wunit_k1) = 0.039         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2748 r_free = 0.2748    target_work(ls_wunit_k1) = 0.039         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2748
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8901
moved from start:          0.2352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11617  Z= 0.122
  Angle     :  0.535  12.533  15810  Z= 0.269
  Chirality :  0.039   0.209   1774
  Planarity :  0.004   0.044   1953
  Dihedral  :  9.644  73.149   1768
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 15.84 %
    Favored  : 82.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.97 (0.23), residues: 1345
  helix:  2.14 (0.21), residues: 619
  sheet: -0.30 (0.43), residues: 121
  loop : -0.76 (0.25), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 545 
 TYR   0.018   0.001   TYR B 533 
 PHE   0.031   0.001   PHE C  41 
 TRP   0.010   0.001   TRP A 336 
 HIS   0.023   0.001   HIS C  51 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00280 /  0.12 (11617)
  covalent geometry    : angle       0.53480 /  0.27 (15810)
  hydrogen bonds       : bond        0.03299 /  2.22 (  533)
  hydrogen bonds       : angle       4.24603 /  3.03 ( 1469)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 69
  time to evaluate  : 0.539 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  617 MET cc_start: 0.8911 (mtm) cc_final: 0.8616 (mtm)
REVERT: B  652 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8397 (tt0)
REVERT: C  101 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7935 (tt)
  outliers start: 25
  outliers final: 22
  residues processed: 83
  average time/residue: 0.0747
  time to fit residues: 10.0190
Evaluate side-chains
  93 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 69
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  483 PHE
Chi-restraints excluded: chain A residue  574 MET
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   32 THR
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  395 MET
Chi-restraints excluded: chain B residue  399 THR
Chi-restraints excluded: chain B residue  407 SER
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain B residue  649 LEU
Chi-restraints excluded: chain B residue  652 GLU
Chi-restraints excluded: chain C residue   51 HIS
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  146 MET
Chi-restraints excluded: chain C residue  181 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 115 optimal weight:    0.0050
   chunk 55 optimal weight:    0.9980
   chunk 135 optimal weight:   10.0000
   chunk 20 optimal weight:    0.6980
   chunk 15 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 34 optimal weight:    0.6980
   chunk 119 optimal weight:    0.6980
   chunk 127 optimal weight:    0.9990
   overall best weight:    0.6194

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  51 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.051943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.039604 restraints weight = 77195.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.2771 rms_B_bonded: 4.21
r_work: 0.2604 rms_B_bonded: 4.74 restraints_weight: 0.5000
r_work (final): 0.2604
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2609
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2609 r_free = 0.2609    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2609 r_free = 0.2609    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2609
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8964
moved from start:          0.2390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  11617  Z= 0.106
  Angle     :  0.542  12.646  15810  Z= 0.271
  Chirality :  0.038   0.206   1774
  Planarity :  0.004   0.045   1953
  Dihedral  :  9.643  73.175   1768
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 15.76 %
    Favored  : 82.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.23), residues: 1345
  helix:  2.13 (0.21), residues: 623
  sheet: -0.26 (0.44), residues: 121
  loop : -0.75 (0.25), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  43 
 TYR   0.017   0.001   TYR B 533 
 PHE   0.031   0.001   PHE C  41 
 TRP   0.010   0.001   TRP A 336 
 HIS   0.033   0.001   HIS C  51 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00238 /  0.11 (11617)
  covalent geometry    : angle       0.54228 /  0.27 (15810)
  hydrogen bonds       : bond        0.03212 /  2.15 (  533)
  hydrogen bonds       : angle       4.21304 /  3.01 ( 1469)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2122.53 seconds
wall clock time: 37 minutes 21.42 seconds (2241.42 seconds total)